406 Open source projects that are alternatives of or similar to awesome-phages

A scalable bacterial genome assembly, annotation and analysis pipeline

A repository for setting up a RNAseq workflow

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Tools for working with genomic and high throughput sequencing data.

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

Remote protein homology detection suite.

Bioconductor cheat sheet

💾 📃 "Reads to report" for public health and clinical microbiology

BioGrakn Knowledge Graph

An ultrafast memory-efficient short read aligner

MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.

A permissively licensed library designed to replace Illumina's Experiment Manager

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

A curated list of bioinformatics bench-marking papers and resources.

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

🔬 BEDOPS: high-performance genomic feature operations

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Bayesian haplotype-based mutation calling

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

A comprehensive library for computational molecular biology

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Fast multi-line FASTA/Q reader in several programming languages

code for reading and processing Allen Institute for Brain Science data

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

A powerful open source data warehouse system

ECG classification programs based on ML/DL methods

Haplotype VCF comparison tools

Code examples of fast and simple k-mer counters for tutorial purposes

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A tool to circularize genome assemblies

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

NGLess: NGS with less work

A curated list of Cheminformatics libraries and software.

A cool place to store your Hi-C

GenomeTools genome analysis system.

Bio4j abstract model and general entry point to the project

Genomics using open source tools, running on GCP or AWS

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Protein Graph Library

Python module for average nucleotide identity analyses

Official git repository for Biopython (originally converted from CVS)

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Python for Bioinformatics

SortMeRNA: next-generation sequence filtering and alignment tool

A faster lmm for GWAS. Supports GPU backend.

Genome assembly evaluation tool

Ten Quick Tips for Deep Learning in Biology

dysgu-SV is a collection of tools for calling structural variants using short or long reads

The BridgeDb Library source code

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

A simple command-line tool to download data from Joint Genome Institute databases

Strelka2 germline and somatic small variant caller